Pre-processing of the data

ls_preprocessed <- preprocess_rna(path_rnaseq = 'rnaseq.RData', correct_batch = T, correct_gender = T)

Exploring data

Batch effect correction

print(ls_preprocessed$pbatch_bf)

print(ls_preprocessed$pgender_bf)

print(ls_preprocessed$pbatch_af)

print(ls_preprocessed$pgender_af)

DE analysis

DE_res <- DE_analysis(ls_preprocessed, 
           GeneBased=TRUE, 
           pDataBased=FALSE,
           NewCondition=FALSE,
           cond_nm='ENSG00000151012.9',
           reference = 'low', 
           correct_gender=TRUE,
           extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1895 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
## 
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done

DE results

heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
  arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- c('ENSG00000250033.1', 'ENSG00000151012.9')
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='SLC7A11', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)

vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
baseMean log2FoldChange lfcSE stat pvalue padj gene symbol Sig lab xvals yvals
74.190171 3.405788 0.2970759 3.381561 0.0007208 0.0278326 ENSG00000070985.9 TRPM5 FC_P TRPM5 3.405788 0.0007208
459.330155 3.027988 0.3489373 8.916714 0.0000000 0.0000000 ENSG00000272405.1 RP11-284F21.10 FC_P RP11.284F21.10 3.027988 0.0000000
7427.904523 3.006456 0.3492571 8.836991 0.0000000 0.0000000 ENSG00000187134.8 AKR1C1 FC_P AKR1C1 3.006456 0.0000000
232.584131 2.999641 0.3634148 8.670954 0.0000000 0.0000000 ENSG00000272068.1 RP11-284F21.9 FC_P RP11.284F21.9 2.999641 0.0000000
479.119508 2.981368 0.3392760 8.829212 0.0000000 0.0000000 ENSG00000171658.4 RP11-443P15.2 FC_P RP11.443P15.2 2.981368 0.0000000
45.882785 2.844477 0.3685875 8.175402 0.0000000 0.0000000 ENSG00000267354.1 RP11-749H17.2 FC_P RP11.749H17.2 2.844477 0.0000000
347.932687 2.805225 0.3518530 8.121889 0.0000000 0.0000000 ENSG00000132874.9 SLC14A2 FC_P SLC14A2 2.805225 0.0000000
3.559773 2.648320 0.3759864 4.796590 0.0000016 0.0004034 ENSG00000223440.1 RP11-555J4.4 FC_P RP11.555J4.4 2.648320 0.0000016
123.368039 2.584478 0.3725841 7.494079 0.0000000 0.0000000 ENSG00000266968.1 RP11-116O18.1 FC_P RP11.116O18.1 2.584478 0.0000000
279.531205 2.546159 0.3487764 7.071791 0.0000000 0.0000000 ENSG00000186529.10 CYP4F3 FC_P CYP4F3 2.546159 0.0000000
4.882729 2.503333 0.3766314 4.880883 0.0000011 0.0002733 ENSG00000230516.1 RP11-555J4.3 FC_P RP11.555J4.3 2.503333 0.0000011
1651.565726 2.497583 0.3473948 7.235067 0.0000000 0.0000000 ENSG00000074410.9 CA12 FC_P CA12 2.497583 0.0000000
870.137624 2.465815 0.3498300 7.118855 0.0000000 0.0000000 ENSG00000023839.6 ABCC2 FC_P ABCC2 2.465815 0.0000000
874.243059 2.463836 0.3688451 7.025027 0.0000000 0.0000000 ENSG00000188517.10 COL25A1 FC_P COL25A1 2.463836 0.0000000
121.539700 2.435846 0.3596729 6.978479 0.0000000 0.0000000 ENSG00000266988.1 RP11-749H17.1 FC_P RP11.749H17.1 2.435846 0.0000000
204.766447 2.424232 0.3165917 7.738857 0.0000000 0.0000000 ENSG00000132692.14 BCAN FC_P BCAN 2.424232 0.0000000
1495.204721 2.399995 0.3443518 7.320679 0.0000000 0.0000000 ENSG00000154277.8 UCHL1 FC_P UCHL1 2.399995 0.0000000
62.349552 2.382709 0.3475235 6.891168 0.0000000 0.0000000 ENSG00000229953.1 RP11-284F21.7 FC_P RP11.284F21.7 2.382709 0.0000000
6545.823063 2.371212 0.3765497 7.174525 0.0000000 0.0000000 ENSG00000021826.10 CPS1 FC_P CPS1 2.371212 0.0000000
465.695914 2.366098 0.3562091 6.746753 0.0000000 0.0000000 ENSG00000198732.6 SMOC1 FC_P SMOC1 2.366098 0.0000000
38.733029 2.343681 0.3502032 6.947071 0.0000000 0.0000000 ENSG00000260253.1 RP4-676L2.1 FC_P RP4.676L2.1 2.343681 0.0000000
80.438655 2.342847 0.3183119 4.513350 0.0000064 0.0011696 ENSG00000123999.4 INHA FC_P INHA 2.342847 0.0000064
110.170354 -2.341944 0.3508471 -4.112740 0.0000391 0.0043567 ENSG00000142319.14 SLC6A3 FC_P SLC6A3 -2.341944 0.0000391
88.568776 2.322626 0.3301606 3.988584 0.0000665 0.0062198 ENSG00000111432.4 FZD10 FC_P FZD10 2.322626 0.0000665
29.331747 2.306891 0.3754437 6.805462 0.0000000 0.0000000 ENSG00000223784.1 RP11-554I8.2 FC_P RP11.554I8.2 2.306891 0.0000000
1274.086656 2.305160 0.3689645 7.243346 0.0000000 0.0000000 ENSG00000163993.6 S100P FC_P S100P 2.305160 0.0000000
362.457374 2.288372 0.3708839 6.370850 0.0000000 0.0000002 ENSG00000145920.10 CPLX2 FC_P CPLX2 2.288372 0.0000000
993.442925 2.286053 0.3768588 7.832738 0.0000000 0.0000000 ENSG00000198074.5 AKR1B10 FC_P AKR1B10 2.286053 0.0000000
642.005472 2.282440 0.3658758 6.538870 0.0000000 0.0000001 ENSG00000162006.5 MSLNL FC_P MSLNL 2.282440 0.0000000
10.306929 2.277901 0.3759199 5.799766 0.0000000 0.0000037 ENSG00000237922.1 RP11-478H16.1 FC_P RP11.478H16.1 2.277901 0.0000000
4.431762 -2.258036 0.3088657 -3.954290 0.0000768 0.0066699 ENSG00000264169.1 RN7SL665P FC_P RN7SL665P -2.258036 0.0000768
694.601993 2.251461 0.3494746 6.537153 0.0000000 0.0000001 ENSG00000113924.7 HGD FC_P HGD 2.251461 0.0000000
50.160905 2.233866 0.3770108 6.607034 0.0000000 0.0000001 ENSG00000204529.3 GUCY2EP FC_P GUCY2EP 2.233866 0.0000000
59.794339 2.225074 0.3589528 4.201972 0.0000265 0.0032623 ENSG00000234854.1 LINC00676 FC_P LINC00676 2.225074 0.0000265
30.274878 2.214739 0.3769530 6.506383 0.0000000 0.0000001 ENSG00000150201.10 FXYD4 FC_P FXYD4 2.214739 0.0000000
529.247003 2.210036 0.3661251 5.881068 0.0000000 0.0000024 ENSG00000171903.12 CYP4F11 FC_P CYP4F11 2.210036 0.0000000
294.213510 2.204818 0.3007350 4.931953 0.0000008 0.0002238 ENSG00000188385.7 JAKMIP3 FC_P JAKMIP3 2.204818 0.0000008
72.955735 2.148765 0.3614406 6.069562 0.0000000 0.0000009 ENSG00000238840.1 U8 FC_P U8 2.148765 0.0000000
15.310757 2.119574 0.3767345 5.995955 0.0000000 0.0000013 ENSG00000266670.1 RN7SL637P FC_P RN7SL637P 2.119574 0.0000000
1395.160446 2.112028 0.3456262 6.104160 0.0000000 0.0000008 ENSG00000163053.6 SLC16A14 FC_P SLC16A14 2.112028 0.0000000
82.463824 2.099401 0.3182834 6.569299 0.0000000 0.0000001 ENSG00000169684.9 CHRNA5 FC_P CHRNA5 2.099401 0.0000000
181.893588 2.096907 0.3563406 5.951120 0.0000000 0.0000017 ENSG00000206633.1 SNORA80B FC_P SNORA80B 2.096907 0.0000000
76.409511 2.077665 0.3762764 6.370548 0.0000000 0.0000002 ENSG00000254632.1 RP11-21L23.4 FC_P RP11.21L23.4 2.077665 0.0000000
6371.061506 2.071104 0.3291870 6.305977 0.0000000 0.0000003 ENSG00000115758.8 ODC1 FC_P ODC1 2.071104 0.0000000
375.318850 2.065094 0.3349679 6.265065 0.0000000 0.0000003 ENSG00000151322.14 NPAS3 FC_P NPAS3 2.065094 0.0000000
230.710001 2.063787 0.3574696 5.982812 0.0000000 0.0000014 ENSG00000074211.9 PPP2R2C FC_P PPP2R2C 2.063787 0.0000000
17.948421 2.036933 0.3736248 4.989893 0.0000006 0.0001779 ENSG00000160182.2 TFF1 FC_P TFF1 2.036933 0.0000006
3379.164215 2.031917 0.3081060 6.658004 0.0000000 0.0000000 ENSG00000181019.8 NQO1 FC_P NQO1 2.031917 0.0000000
71.367166 2.031584 0.3753486 5.822359 0.0000000 0.0000033 ENSG00000258346.1 RP11-148B3.2 FC_P RP11.148B3.2 2.031584 0.0000000
17.710673 2.029457 0.3718034 3.410167 0.0006492 0.0259320 ENSG00000258657.1 RP11-104E19.1 FC_P RP11.104E19.1 2.029457 0.0006492
1402.099877 2.025799 0.3683234 5.713581 0.0000000 0.0000055 ENSG00000081277.7 PKP1 FC_P PKP1 2.025799 0.0000000
1046.315215 2.022021 0.3444501 5.946139 0.0000000 0.0000017 ENSG00000006016.6 CRLF1 FC_P CRLF1 2.022021 0.0000000
2.508772 2.020757 0.3764879 5.375034 0.0000001 0.0000304 ENSG00000267909.1 CCDC177 FC_P CCDC177 2.020757 0.0000001
2428.113741 2.005371 0.3154303 6.305759 0.0000000 0.0000003 ENSG00000159228.8 CBR1 FC_P CBR1 2.005371 0.0000000
37.599176 2.002212 0.3574304 3.349147 0.0008106 0.0301553 ENSG00000101076.12 HNF4A FC_P HNF4A 2.002212 0.0008106
255.242400 1.996612 0.3732896 6.206375 0.0000000 0.0000004 ENSG00000196091.8 MYBPC1 FC_P MYBPC1 1.996612 0.0000000
3.302264 1.987676 0.3762094 5.588683 0.0000000 0.0000107 ENSG00000249199.1 CTD-2139B15.5 FC_P CTD.2139B15.5 1.987676 0.0000000
19.305845 1.976134 0.3762142 5.567895 0.0000000 0.0000118 ENSG00000237937.1 AP000770.1 FC_P AP000770.1 1.976134 0.0000000
10.903050 1.972538 0.3751092 6.067071 0.0000000 0.0000009 ENSG00000164089.4 ETNPPL FC_P ETNPPL 1.972538 0.0000000
95.226916 1.972021 0.3521824 5.041675 0.0000005 0.0001415 ENSG00000156755.9 IGKV1OR-2 FC_P IGKV1OR.2 1.972021 0.0000005
160.927856 1.969863 0.3619607 4.344289 0.0000140 0.0020543 ENSG00000171759.4 PAH FC_P PAH 1.969863 0.0000140
194.766130 1.968949 0.3570444 5.549415 0.0000000 0.0000128 ENSG00000174473.11 GALNTL6 FC_P GALNTL6 1.968949 0.0000000
50.443154 1.954590 0.3676189 5.376872 0.0000001 0.0000304 ENSG00000237810.3 CTD-2571E19.3 FC_P CTD.2571E19.3 1.954590 0.0000001
21.973522 1.950368 0.3748841 6.086028 0.0000000 0.0000008 ENSG00000238001.2 RP11-555J4.2 FC_P RP11.555J4.2 1.950368 0.0000000
69.201905 1.945125 0.3760332 5.245463 0.0000002 0.0000587 ENSG00000267056.2 AC005336.4 FC_P AC005336.4 1.945125 0.0000002
21.896080 1.935212 0.3732443 5.238493 0.0000002 0.0000598 ENSG00000199400.1 RNY4P19 FC_P RNY4P19 1.935212 0.0000002
209.780583 1.928813 0.3432631 5.569095 0.0000000 0.0000118 ENSG00000166206.9 GABRB3 FC_P GABRB3 1.928813 0.0000000
8.383895 1.925363 0.3733169 6.059844 0.0000000 0.0000009 ENSG00000266952.1 RP11-909B2.1 FC_P RP11.909B2.1 1.925363 0.0000000
866.222931 1.917266 0.2860782 6.760482 0.0000000 0.0000000 ENSG00000176153.10 GPX2 FC_P GPX2 1.917266 0.0000000
21.006391 1.913548 0.3622107 5.380539 0.0000001 0.0000301 ENSG00000248802.1 RP11-184M15.2 FC_P RP11.184M15.2 1.913548 0.0000001
87.069743 1.913200 0.3207755 5.943249 0.0000000 0.0000017 ENSG00000268657.1 AL133373.1 FC_P AL133373.1 1.913200 0.0000000
619.702039 1.912097 0.3328342 5.638360 0.0000000 0.0000082 ENSG00000160211.11 G6PD FC_P G6PD 1.912097 0.0000000
219.862687 1.880657 0.3468073 5.493415 0.0000000 0.0000171 ENSG00000105696.4 TMEM59L FC_P TMEM59L 1.880657 0.0000000
834.025114 1.880009 0.3763159 6.216487 0.0000000 0.0000004 ENSG00000125851.5 PCSK2 FC_P PCSK2 1.880009 0.0000000
1320.572201 1.877303 0.3352290 5.617172 0.0000000 0.0000092 ENSG00000196208.9 GREB1 FC_P GREB1 1.877303 0.0000000
857.358271 1.875697 0.3767609 5.955880 0.0000000 0.0000017 ENSG00000223414.2 LINC00473 FC_P LINC00473 1.875697 0.0000000
15.339345 1.868028 0.3521888 5.257173 0.0000001 0.0000556 ENSG00000235010.1 RP11-140A10.3 FC_P RP11.140A10.3 1.868028 0.0000001
1011.557633 1.864581 0.3281571 5.784366 0.0000000 0.0000039 ENSG00000088992.13 TESC FC_P TESC 1.864581 0.0000000
28.704369 -1.858401 0.3742610 -4.989742 0.0000006 0.0001779 ENSG00000253998.2 IGKV2-29 FC_P IGKV2.29 -1.858401 0.0000006
26.352033 1.855965 0.2869215 6.435439 0.0000000 0.0000001 ENSG00000238266.1 LINC00707 FC_P LINC00707 1.855965 0.0000000
241.237536 1.843452 0.3741078 6.405012 0.0000000 0.0000002 ENSG00000256391.1 SDIM1 FC_P SDIM1 1.843452 0.0000000
6.520975 1.839244 0.3670198 4.975890 0.0000006 0.0001881 ENSG00000213877.3 CFL1P7 FC_P CFL1P7 1.839244 0.0000006
3590.008024 1.838267 0.3210254 5.721048 0.0000000 0.0000053 ENSG00000108551.4 RASD1 FC_P RASD1 1.838267 0.0000000
459.443327 1.833677 0.3605677 5.212133 0.0000002 0.0000681 ENSG00000130234.6 ACE2 FC_P ACE2 1.833677 0.0000002
7491.793041 1.825854 0.3656628 5.129465 0.0000003 0.0000973 ENSG00000102854.10 MSLN FC_P MSLN 1.825854 0.0000003
389.824841 1.816518 0.2906246 6.269368 0.0000000 0.0000003 ENSG00000154040.16 CABYR FC_P CABYR 1.816518 0.0000000
455.267267 1.803813 0.3770193 5.392606 0.0000001 0.0000288 ENSG00000173702.3 MUC13 FC_P MUC13 1.803813 0.0000001
54.320259 1.787927 0.3709747 6.165040 0.0000000 0.0000006 ENSG00000254761.1 RP11-672A2.1 FC_P RP11.672A2.1 1.787927 0.0000000
47.113664 1.769783 0.3395574 4.937011 0.0000008 0.0002210 ENSG00000103154.5 NECAB2 FC_P NECAB2 1.769783 0.0000008
11.489322 1.754215 0.3709195 4.909610 0.0000009 0.0002432 ENSG00000261146.1 RP11-2A4.4 FC_P RP11.2A4.4 1.754215 0.0000009
124.663437 1.748197 0.3201227 5.486194 0.0000000 0.0000176 ENSG00000138152.7 BTBD16 FC_P BTBD16 1.748197 0.0000000
6.366272 -1.746772 0.3679698 -4.403550 0.0000106 0.0017046 ENSG00000235712.6 RXRB FC_P RXRB -1.746772 0.0000106
31.092473 1.740834 0.3028418 5.746033 0.0000000 0.0000048 ENSG00000227184.3 EPPK1 FC_P EPPK1 1.740834 0.0000000
35.256486 -1.740491 0.3529971 -4.750027 0.0000020 0.0004883 ENSG00000249320.1 RP11-206P5.1 FC_P RP11.206P5.1 -1.740491 0.0000020
114.416012 1.732618 0.3581048 4.261021 0.0000203 0.0027303 ENSG00000086159.8 AQP6 FC_P AQP6 1.732618 0.0000203
4000.175504 1.726165 0.2671587 6.482953 0.0000000 0.0000001 ENSG00000109814.7 UGDH FC_P UGDH 1.726165 0.0000000
7.630741 1.723931 0.3768766 4.678865 0.0000029 0.0006419 ENSG00000254975.1 RP11-672A2.3 FC_P RP11.672A2.3 1.723931 0.0000029
6.528918 1.720410 0.3702455 4.720316 0.0000024 0.0005455 ENSG00000237838.1 AC133680.1 FC_P AC133680.1 1.720410 0.0000024
6.637467 1.708287 0.3765066 4.949911 0.0000007 0.0002100 ENSG00000231295.1 RP4-797C5.2 FC_P RP4.797C5.2 1.708287 0.0000007
47.601009 1.702250 0.3530480 4.736376 0.0000022 0.0005168 ENSG00000179477.5 ALOX12B FC_P ALOX12B 1.702250 0.0000022
11.504493 1.700148 0.3589490 4.763558 0.0000019 0.0004628 ENSG00000235899.1 RP11-345L23.1 FC_P RP11.345L23.1 1.700148 0.0000019
7.118675 1.694329 0.3690801 4.592801 0.0000044 0.0008775 ENSG00000224409.1 RP11-114B7.6 FC_P RP11.114B7.6 1.694329 0.0000044
66.019409 1.691193 0.3227927 5.121348 0.0000003 0.0001006 ENSG00000080644.11 CHRNA3 FC_P CHRNA3 1.691193 0.0000003
21.569154 1.686967 0.3450868 4.807041 0.0000015 0.0003855 ENSG00000261762.1 RP11-650L12.2 FC_P RP11.650L12.2 1.686967 0.0000015
400.284587 1.681043 0.2796218 5.948558 0.0000000 0.0000017 ENSG00000108448.16 TRIM16L FC_P TRIM16L 1.681043 0.0000000
72.167854 1.680654 0.3447147 4.560148 0.0000051 0.0009818 ENSG00000132437.13 DDC FC_P DDC 1.680654 0.0000051
954.309668 1.673960 0.2362214 3.528497 0.0004179 0.0198333 ENSG00000182704.6 TSKU FC_P TSKU 1.673960 0.0004179
98.576368 -1.671048 0.3411904 -5.182546 0.0000002 0.0000776 ENSG00000164530.9 PI16 FC_P PI16 -1.671048 0.0000002
4.408143 1.665405 0.3658897 4.468331 0.0000079 0.0013468 ENSG00000215124.2 RP3-420J14.1 FC_P RP3.420J14.1 1.665405 0.0000079
16736.465458 1.664487 0.3770252 4.734241 0.0000022 0.0005177 ENSG00000096088.12 PGC FC_P PGC 1.664487 0.0000022
108.467056 1.653458 0.3746183 4.705612 0.0000025 0.0005702 ENSG00000227471.4 AKR1B15 FC_P AKR1B15 1.653458 0.0000025
689.124594 1.652816 0.2705632 6.098655 0.0000000 0.0000008 ENSG00000255150.1 EID3 FC_P EID3 1.652816 0.0000000
91.644442 1.647355 0.3299786 4.980873 0.0000006 0.0001848 ENSG00000233461.1 RP11-295G20.2 FC_P RP11.295G20.2 1.647355 0.0000006
640.385844 1.635229 0.2587414 6.309197 0.0000000 0.0000003 ENSG00000125775.10 SDCBP2 FC_P SDCBP2 1.635229 0.0000000
394.981996 1.633637 0.3342019 4.960803 0.0000007 0.0002002 ENSG00000137261.9 KIAA0319 FC_P KIAA0319 1.633637 0.0000007
324.554693 1.631043 0.3623638 4.530160 0.0000059 0.0011063 ENSG00000260604.1 RP1-140K8.5 FC_P RP1.140K8.5 1.631043 0.0000059
4.845477 1.623302 0.3768987 4.652562 0.0000033 0.0007079 ENSG00000253182.1 RP11-486M23.2 FC_P RP11.486M23.2 1.623302 0.0000033
305.596281 1.621391 0.3756554 4.353121 0.0000134 0.0019910 ENSG00000139144.5 PIK3C2G FC_P PIK3C2G 1.621391 0.0000134
30.625669 1.619772 0.2995074 5.401982 0.0000001 0.0000276 ENSG00000207951.1 MIR561 FC_P MIR561 1.619772 0.0000001
15.391692 -1.611632 0.3769907 -4.671517 0.0000030 0.0006573 ENSG00000172782.7 FADS6 FC_P FADS6 -1.611632 0.0000030
28.058468 1.604897 0.3706982 4.327717 0.0000151 0.0021562 ENSG00000225365.1 AC078942.1 FC_P AC078942.1 1.604897 0.0000151
924.026965 1.594844 0.3112693 5.167927 0.0000002 0.0000823 ENSG00000152049.5 KCNE4 FC_P KCNE4 1.594844 0.0000002
130.255646 1.587408 0.3716887 4.140020 0.0000347 0.0039907 ENSG00000139352.3 ASCL1 FC_P ASCL1 1.587408 0.0000347
893.612664 1.584746 0.3066767 5.140070 0.0000003 0.0000928 ENSG00000141527.12 CARD14 FC_P CARD14 1.584746 0.0000003
56.094917 1.583818 0.3622893 4.529537 0.0000059 0.0011063 ENSG00000267097.1 RP11-309E23.2 FC_P RP11.309E23.2 1.583818 0.0000059
519.897668 1.579999 0.2686068 5.841001 0.0000000 0.0000030 ENSG00000140961.8 OSGIN1 FC_P OSGIN1 1.579999 0.0000000
434.077514 1.576655 0.3269303 4.774475 0.0000018 0.0004413 ENSG00000188660.3 LINC00319 FC_P LINC00319 1.576655 0.0000018
70.279417 1.574257 0.3572117 4.608540 0.0000041 0.0008361 ENSG00000237289.5 CKMT1B FC_P CKMT1B 1.574257 0.0000041
40.675955 1.569777 0.3727069 4.209043 0.0000256 0.0032052 ENSG00000182256.8 GABRG3 FC_P GABRG3 1.569777 0.0000256
164.153848 -1.566624 0.3380011 -3.640008 0.0002726 0.0153539 ENSG00000178343.4 SHISA3 FC_P SHISA3 -1.566624 0.0002726
311.466074 1.561926 0.3236758 4.930127 0.0000008 0.0002238 ENSG00000168772.9 CXXC4 FC_P CXXC4 1.561926 0.0000008
4.667776 1.560918 0.3705970 4.465947 0.0000080 0.0013468 ENSG00000226122.1 AC018705.5 FC_P AC018705.5 1.560918 0.0000080
2.248005 1.558301 0.3652640 3.610291 0.0003059 0.0162947 ENSG00000249771.1 RP11-457P14.5 FC_P RP11.457P14.5 1.558301 0.0003059
53.491602 1.556404 0.3616656 4.663674 0.0000031 0.0006747 ENSG00000236345.1 RP11-59D5__B.2 FC_P RP11.59D5__B.2 1.556404 0.0000031
24.203147 1.545563 0.3759043 4.585414 0.0000045 0.0008986 ENSG00000253789.1 CTD-2571E19.1 FC_P CTD.2571E19.1 1.545563 0.0000045
18.804877 1.544589 0.3648193 3.977194 0.0000697 0.0063148 ENSG00000122711.4 SPINK4 FC_P SPINK4 1.544589 0.0000697
17.496912 1.543927 0.3641707 5.565284 0.0000000 0.0000118 ENSG00000236627.1 RP11-252P19.1 FC_P RP11.252P19.1 1.543927 0.0000000
3143.845023 1.541651 0.3770657 4.507479 0.0000066 0.0011794 ENSG00000108602.13 ALDH3A1 FC_P ALDH3A1 1.541651 0.0000066
12.035027 1.537615 0.3480180 4.377730 0.0000120 0.0018623 ENSG00000268791.1 AC093323.1 FC_P AC093323.1 1.537615 0.0000120
43.000719 1.535024 0.3611163 3.879784 0.0001045 0.0082697 ENSG00000117971.7 CHRNB4 FC_P CHRNB4 1.535024 0.0001045
718.846094 1.530922 0.2918438 5.188078 0.0000002 0.0000760 ENSG00000101311.11 FERMT1 FC_P FERMT1 1.530922 0.0000002
3439.676426 1.529067 0.2882660 5.296498 0.0000001 0.0000458 ENSG00000001084.6 GCLC FC_P GCLC 1.529067 0.0000001
13.422176 1.527770 0.3526101 4.197867 0.0000269 0.0032823 ENSG00000234427.1 RP3-413H6.2 FC_P RP3.413H6.2 1.527770 0.0000269
388.632248 1.524274 0.3359375 4.568900 0.0000049 0.0009568 ENSG00000002726.15 AOC1 FC_P AOC1 1.524274 0.0000049
122.097272 1.523625 0.2904462 5.280863 0.0000001 0.0000494 ENSG00000271303.1 SRXN1 FC_P SRXN1 1.523625 0.0000001
162.336916 1.520657 0.3698228 4.272616 0.0000193 0.0026605 ENSG00000220154.2 RP11-46B11.2 FC_P RP11.46B11.2 1.520657 0.0000193
39.369008 1.519626 0.3308175 4.439335 0.0000090 0.0014901 ENSG00000230212.2 AP000688.14 FC_P AP000688.14 1.519626 0.0000090
24.272149 1.517845 0.3669766 4.669163 0.0000030 0.0006609 ENSG00000124102.4 PI3 FC_P PI3 1.517845 0.0000030
36.434622 1.513468 0.3750946 4.135713 0.0000354 0.0040229 ENSG00000260658.1 RP11-368L12.1 FC_P RP11.368L12.1 1.513468 0.0000354
7.562996 1.512713 0.3735174 3.947926 0.0000788 0.0067374 ENSG00000255993.1 PSMC1P9 FC_P PSMC1P9 1.512713 0.0000788
12.687357 1.511256 0.3673983 4.335138 0.0000146 0.0021095 ENSG00000146678.5 IGFBP1 FC_P IGFBP1 1.511256 0.0000146
71.579732 1.507560 0.3444255 4.263853 0.0000201 0.0027058 ENSG00000259425.1 RP11-566K19.5 FC_P RP11.566K19.5 1.507560 0.0000201
726.718346 1.506727 0.2870542 5.238100 0.0000002 0.0000598 ENSG00000166126.6 AMN FC_P AMN 1.506727 0.0000002
3.503468 1.506585 0.3719346 4.048331 0.0000516 0.0052438 ENSG00000249887.1 RP11-457P14.6 FC_P RP11.457P14.6 1.506585 0.0000516
53.588664 -1.504691 0.3755506 -4.092375 0.0000427 0.0045854 ENSG00000189127.3 ANKRD34B FC_P ANKRD34B -1.504691 0.0000427
34.159138 -1.504641 0.3561157 -4.234575 0.0000229 0.0029739 ENSG00000206176.5 AC023490.1 FC_P AC023490.1 -1.504641 0.0000229
97.925630 1.504343 0.3757152 4.256290 0.0000208 0.0027785 ENSG00000201464.1 Y_RNA FC_P Y_RNA 1.504343 0.0000208
4.532727 1.501453 0.3723273 4.033832 0.0000549 0.0054566 ENSG00000218813.1 RP11-59D5__B.3 FC_P RP11.59D5__B.3 1.501453 0.0000549

Pathway enrichment analysis fGSEA

Low SLC7A11 is the reference. When SLC7A11 is high, pathways shown below are up- or down- regulated

fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
HALLMARK_MYC_TARGETS_V1 0.0013793 0.0048450 0.5760355 2.663927 0 189 up
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0014225 0.0048450 0.5345159 2.429883 0 175 up
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY 0.0015504 0.0048450 0.6106734 2.228717 0 46 up
HALLMARK_MYC_TARGETS_V2 0.0015385 0.0048450 0.5836289 2.207744 0 57 up
HALLMARK_MTORC1_SIGNALING 0.0013812 0.0048450 0.4708370 2.175679 0 190 up
HALLMARK_E2F_TARGETS 0.0013812 0.0048450 0.4544360 2.099844 0 191 up
HALLMARK_FATTY_ACID_METABOLISM 0.0014286 0.0048450 0.4673342 2.075779 0 147 up
HALLMARK_GLYCOLYSIS 0.0013774 0.0048450 0.4445459 2.055879 0 188 up
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.0014599 0.0048450 0.4911549 2.052527 0 103 up
HALLMARK_XENOBIOTIC_METABOLISM 0.0013774 0.0048450 0.4289172 1.983601 0 188 up
HALLMARK_G2M_CHECKPOINT 0.0013870 0.0048450 0.4081273 1.881154 0 187 up
HALLMARK_P53_PATHWAY 0.0013812 0.0048450 0.3842814 1.775717 0 190 up
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0013793 0.0048450 0.3800266 1.760757 0 193 up
HALLMARK_ESTROGEN_RESPONSE_EARLY 0.0013812 0.0048450 0.3527743 1.630089 0 191 up
HALLMARK_ADIPOGENESIS 0.0013870 0.0048450 0.3516720 1.618148 0 183 up
HALLMARK_DNA_REPAIR 0.0014245 0.0048450 0.3592588 1.584524 0 141 up
HALLMARK_ALLOGRAFT_REJECTION 0.0035587 0.0064935 -0.6380091 -3.203795 0 187 down
HALLMARK_INTERFERON_GAMMA_RESPONSE 0.0036364 0.0064935 -0.6219276 -3.127702 0 194 down
HALLMARK_INTERFERON_ALPHA_RESPONSE 0.0031056 0.0064935 -0.6655971 -3.038984 0 93 down
HALLMARK_IL6_JAK_STAT3_SIGNALING 0.0029851 0.0064935 -0.5915983 -2.654658 0 82 down
HALLMARK_INFLAMMATORY_RESPONSE 0.0036101 0.0064935 -0.5211774 -2.623153 0 193 down
HALLMARK_IL2_STAT5_SIGNALING 0.0035971 0.0064935 -0.4470018 -2.246278 0 190 down
HALLMARK_COMPLEMENT 0.0036101 0.0064935 -0.3962333 -1.994293 0 193 down
HALLMARK_KRAS_SIGNALING_UP 0.0035971 0.0064935 -0.3913819 -1.966777 0 190 down
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0036364 0.0064935 -0.3794807 -1.912989 0 195 down
HALLMARK_MYOGENESIS 0.0035971 0.0064935 -0.3569952 -1.793976 0 190 down
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0036101 0.0064935 -0.3546836 -1.773415 0 189 down
HALLMARK_PROTEIN_SECRETION 0.0029586 0.0064935 0.3780810 1.544232 1 89 up
HALLMARK_APOPTOSIS 0.0067114 0.0115714 -0.3245534 -1.594300 1 155 down
HALLMARK_PANCREAS_BETA_CELLS 0.0272000 0.0453333 0.4285979 1.466396 16 36 up 
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
chr10q26 0.0014881 0.0183214 0.5331844 2.257309 0 108 up
chr1q41 0.0015798 0.0183214 0.5920613 2.213632 0 49 up
chr15q15 0.0014881 0.0183214 0.5171942 2.189613 0 108 up
chr4q25 0.0015974 0.0183214 0.5993173 2.174446 0 43 up
chr4q28 0.0017331 0.0183214 0.6667811 2.133799 0 25 up
chr15q26 0.0015291 0.0183214 0.4981181 2.079024 0 99 up
chr15q25 0.0015385 0.0183214 0.5104607 2.075108 0 84 up
chr6p24 0.0016367 0.0183214 0.5837631 2.062940 0 37 up
chr12q14 0.0016155 0.0183214 0.5366383 2.028993 0 56 up
chr2p25 0.0015649 0.0183214 0.5232161 2.021751 0 61 up
chr15q23 0.0016181 0.0183214 0.5576396 2.007328 0 42 up
chr13q32 0.0015773 0.0183214 0.5100048 1.997452 0 67 up
chr13q34 0.0016000 0.0183214 0.5283381 1.991566 0 54 up
chr20p12 0.0015873 0.0183214 0.5128631 1.963287 0 58 up
MT 0.0016750 0.0183214 0.5741479 1.941781 0 31 up
chr15q22 0.0015723 0.0183214 0.4725615 1.906289 0 82 up
chr12q15 0.0016779 0.0183214 0.5526632 1.901309 0 34 up
chr17p11 0.0014684 0.0183214 0.4409642 1.879412 0 110 up
chr8p22 0.0017331 0.0183214 0.5862340 1.876037 0 25 up
chr4q12 0.0015823 0.0183214 0.4990676 1.872528 0 53 up
chr2q36 0.0015798 0.0183214 0.5056552 1.868338 0 46 up
chr2q37 0.0014286 0.0183214 0.4228101 1.866131 0 138 up
chr1q22 0.0015823 0.0183214 0.4956299 1.859630 0 53 up
chr12p11 0.0016207 0.0183214 0.5173659 1.852060 0 41 up
chr10q24 0.0014514 0.0183214 0.4184415 1.828484 0 127 up
chr15q24 0.0015456 0.0183214 0.4547009 1.812346 0 74 up
chr1q32 0.0013850 0.0183214 0.3973585 1.811982 0 174 up
chr2q21 0.0015773 0.0183214 0.4447608 1.713577 0 60 up
chr5q33 0.0028169 0.0208539 -0.5820298 -2.535771 0 77 down
chrYq11 0.0024691 0.0208539 -0.6315504 -2.276605 0 31 down 
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
FARMER_BREAST_CANCER_CLUSTER_1 0.0028818 0.0196461 -0.8260042 -3.247368 0 47 down
WINTER_HYPOXIA_DN 0.0028011 0.0196461 -0.7893779 -3.098433 0 46 down
LEE_EARLY_T_LYMPHOCYTE_DN 0.0028249 0.0196461 -0.7390486 -3.032090 0 57 down
REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES 0.0028736 0.0196461 -0.7393387 -3.003432 0 55 down
WIELAND_UP_BY_HBV_INFECTION 0.0031153 0.0196461 -0.6559711 -2.998066 0 95 down
FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP 0.0030960 0.0196461 -0.6732522 -2.962720 0 83 down
BASSO_CD40_SIGNALING_UP 0.0031056 0.0196461 -0.6328562 -2.934267 0 100 down
MOSERLE_IFNA_RESPONSE 0.0025773 0.0196461 -0.7977625 -2.910504 0 31 down
KEGG_HEMATOPOIETIC_CELL_LINEAGE 0.0029499 0.0196461 -0.6521875 -2.862517 0 80 down
PID_CD8_TCR_PATHWAY 0.0028818 0.0196461 -0.7084363 -2.841749 0 51 down
REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_BCR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS 0.0029499 0.0196461 -0.6441142 -2.835918 0 81 down
BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE 0.0029762 0.0196461 -0.6538299 -2.826034 0 74 down
HECKER_IFNB1_TARGETS 0.0029851 0.0196461 -0.6220923 -2.825893 0 90 down
BROWNE_INTERFERON_RESPONSIVE_GENES 0.0029412 0.0196461 -0.6713939 -2.818827 0 65 down
BIOCARTA_NKT_PATHWAY 0.0025575 0.0196461 -0.8135376 -2.817425 0 26 down
KLEIN_TARGETS_OF_BCR_ABL1_FUSION 0.0027397 0.0196461 -0.7571254 -2.817384 0 36 down
NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP 0.0029240 0.0196461 -0.6426595 -2.812763 0 78 down
MORI_LARGE_PRE_BII_LYMPHOCYTE_DN 0.0028571 0.0196461 -0.6848839 -2.793748 0 56 down
VILIMAS_NOTCH1_TARGETS_UP 0.0028818 0.0196461 -0.7025690 -2.780732 0 49 down
BIOCARTA_CTLA4_PATHWAY 0.0024814 0.0196461 -0.8352163 -2.779558 0 22 down
PID_TCR_PATHWAY 0.0028653 0.0196461 -0.6683934 -2.776875 0 61 down
KEGG_PRIMARY_IMMUNODEFICIENCY 0.0025773 0.0196461 -0.7611325 -2.776866 0 31 down
DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP 0.0029070 0.0196461 -0.6924999 -2.748421 0 50 down
KEGG_LEISHMANIA_INFECTION 0.0028653 0.0196461 -0.6426038 -2.743560 0 68 down
KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS 0.0027855 0.0196461 -0.7059626 -2.728283 0 43 down
KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION 0.0028818 0.0196461 -0.6931562 -2.725087 0 47 down
PID_IL12_2PATHWAY 0.0028986 0.0196461 -0.6549167 -2.721004 0 63 down
PID_CD8_TCR_DOWNSTREAM_PATHWAY 0.0028736 0.0196461 -0.6644365 -2.699155 0 55 down
REACTOME_INTERLEUKIN_2_FAMILY_SIGNALING 0.0027100 0.0196461 -0.7138463 -2.690848 0 38 down
CROONQUIST_NRAS_SIGNALING_UP 0.0026247 0.0196461 -0.7220709 -2.686291 0 35 down 
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
EPC1_TARGET_GENES 0.0012270 0.0332968 0.4278147 2.071140 0 332 up
DLX6_TARGET_GENES 0.0011848 0.0332968 0.4125402 2.058368 0 486 up
DLX4_TARGET_GENES 0.0011403 0.0332968 0.3894230 1.997025 0 719 up
FOXO4_TARGET_GENES 0.0012300 0.0332968 0.4118343 1.984089 0 314 up
DIDO1_TARGET_GENES 0.0010593 0.0332968 0.3691100 1.956280 0 1381 up
ALKBH3_TARGET_GENES 0.0012121 0.0332968 0.3996774 1.951342 0 382 up
GRHL1_TARGET_GENES 0.0010627 0.0332968 0.3615587 1.915082 0 1334 up
ZNF711_TARGET_GENES 0.0010604 0.0332968 0.3585655 1.902567 0 1465 up
CREB3L4_TARGET_GENES 0.0010672 0.0332968 0.3603724 1.901884 0 1195 up
BARHL1_TARGET_GENES 0.0010753 0.0332968 0.3605334 1.899527 0 1106 up
ZNF250_TARGET_GENES 0.0011820 0.0332968 0.3777457 1.892073 0 512 up
FXR1_TARGET_GENES 0.0010905 0.0332968 0.3604618 1.888812 0 1002 up
HNRNPH1_TARGET_GENES 0.0010604 0.0332968 0.3540523 1.878376 0 1454 up
MXD1_TARGET_GENES 0.0011682 0.0332968 0.3711710 1.869984 0 548 up
FOXG1_TARGET_GENES 0.0011834 0.0332968 0.3733874 1.868001 0 508 up
SUPT20H_TARGET_GENES 0.0010695 0.0332968 0.3514654 1.853684 0 1169 up
BANP_TARGET_GENES 0.0011481 0.0332968 0.3618220 1.843724 0 635 up
KAT5_TARGET_GENES 0.0011211 0.0332968 0.3567611 1.840118 0 768 up
ADA2_TARGET_GENES 0.0011148 0.0332968 0.3541726 1.832291 0 801 up
KLF3_TARGET_GENES 0.0011111 0.0332968 0.3542812 1.832139 0 794 up
NFE2L1_TARGET_GENES 0.0012240 0.0332968 0.3747939 1.831210 0 394 up
HOXA1_TARGET_GENES 0.0010917 0.0332968 0.3481950 1.824570 0 1005 up
SRPK1_TARGET_GENES 0.0012361 0.0332968 0.3772523 1.817414 0 317 up
ATF5_TARGET_GENES 0.0012121 0.0332968 0.3729002 1.815298 0 368 up
BARX1_TARGET_GENES 0.0010823 0.0332968 0.3447329 1.813488 0 1074 up
ELF2_TARGET_GENES 0.0011364 0.0332968 0.3526484 1.809987 0 722 up
ATF6_TARGET_GENES 0.0010989 0.0332968 0.3462504 1.808447 0 918 up
HOXB6_TARGET_GENES 0.0011710 0.0332968 0.3587852 1.803924 0 531 up
SETD1A_TARGET_GENES 0.0010537 0.0332968 0.3401146 1.800749 0 1272 up
TEAD2_TARGET_GENES 0.0010549 0.0332968 0.3393491 1.796229 0 1241 up 
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GNF2_PA2G4 0.0014903 0.0098621 0.6163449 2.464975 0 75 up
GNF2_RAN 0.0014793 0.0098621 0.6081434 2.463487 0 79 up
MORF_SOD1 0.0012563 0.0098621 0.5185047 2.450594 0 247 up
MORF_RFC4 0.0013624 0.0098621 0.5565803 2.444442 0 130 up
MORF_UNG 0.0015083 0.0098621 0.6239810 2.441502 0 64 up
MORF_BUB3 0.0012579 0.0098621 0.5058740 2.388946 0 243 up
MORF_EI24 0.0013966 0.0098621 0.5532820 2.382313 0 119 up
MORF_PPP1CC 0.0013228 0.0098621 0.5257248 2.358548 0 147 up
MORF_HAT1 0.0013210 0.0098621 0.5226613 2.356257 0 155 up
GNF2_RRM1 0.0014663 0.0098621 0.5653797 2.322414 0 86 up
MORF_DNMT1 0.0014245 0.0098621 0.5483406 2.319696 0 103 up
MORF_EIF3S2 0.0012658 0.0098621 0.4955697 2.317422 0 220 up
GNF2_SMC4L1 0.0014859 0.0098621 0.5706785 2.312354 0 80 up
GNF2_PCNA 0.0015198 0.0098621 0.5910762 2.312306 0 65 up
MORF_HDAC2 0.0012563 0.0098621 0.4884997 2.308782 0 247 up
MORF_RRM1 0.0014684 0.0098621 0.5565185 2.295097 0 88 up
GNF2_MCM4 0.0015480 0.0098621 0.6053695 2.280582 0 52 up
MORF_CSNK2B 0.0012516 0.0098621 0.4799630 2.276063 0 258 up
MODULE_286 0.0016260 0.0098621 0.6681389 2.271151 0 34 up
MORF_DAP3 0.0012937 0.0098621 0.4924239 2.269665 0 179 up
MORF_MTA1 0.0014556 0.0098621 0.5465058 2.268571 0 91 up
MORF_FEN1 0.0015576 0.0098621 0.5922271 2.255523 0 55 up
MODULE_235 0.0014706 0.0098621 0.5592473 2.250784 0 77 up
MORF_PRKDC 0.0013441 0.0098621 0.4945365 2.243867 0 166 up
MORF_RAD23A 0.0012315 0.0098621 0.4617755 2.226926 0 304 up
GNF2_CCNA2 0.0015198 0.0098621 0.5672663 2.219162 0 65 up
MODULE_54 0.0012658 0.0098621 0.4710572 2.218779 0 241 up
GNF2_NS 0.0016340 0.0098621 0.6418281 2.218777 0 37 up
MORF_RAN 0.0012626 0.0098621 0.4697997 2.216768 0 239 up
MORF_PTPN11 0.0014430 0.0098621 0.5290984 2.210565 0 94 up 
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GO_T_CELL_RECEPTOR_COMPLEX 0.0030211 0.0421001 -0.7926478 -3.617955 0 90 down
GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION 0.0037313 0.0421001 -0.5934269 -3.057276 0 209 down
GO_RESPONSE_TO_CHEMOKINE 0.0030864 0.0421001 -0.6396210 -2.910984 0 89 down
GO_LYMPHOCYTE_MIGRATION 0.0032258 0.0421001 -0.6272134 -2.870948 0 101 down
GO_POSITIVE_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION 0.0035336 0.0421001 -0.5857222 -2.846517 0 142 down
GO_POSITIVE_REGULATION_OF_LYMPHOCYTE_DIFFERENTIATION 0.0030211 0.0421001 -0.6233623 -2.846017 0 91 down
GO_ALPHA_BETA_T_CELL_DIFFERENTIATION 0.0031646 0.0421001 -0.6205015 -2.837391 0 98 down
GO_IMMUNE_RECEPTOR_ACTIVITY 0.0034130 0.0421001 -0.5973635 -2.820265 0 120 down
GO_ALPHA_BETA_T_CELL_ACTIVATION 0.0034843 0.0421001 -0.5829611 -2.806821 0 131 down
GO_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY 0.0028736 0.0421001 -0.6629003 -2.785785 0 60 down
GO_B_CELL_RECEPTOR_SIGNALING_PATHWAY 0.0032051 0.0421001 -0.6049015 -2.783731 0 103 down
GO_CYTOKINE_RECEPTOR_ACTIVITY 0.0030211 0.0421001 -0.6082884 -2.777196 0 91 down
GO_T_CELL_SELECTION 0.0027701 0.0421001 -0.7051419 -2.770701 0 46 down
GO_REGULATION_OF_LYMPHOCYTE_DIFFERENTIATION 0.0038168 0.0421001 -0.5617022 -2.765002 0 162 down
GO_LYMPHOCYTE_CHEMOTAXIS 0.0028902 0.0421001 -0.6667680 -2.743115 0 55 down
GO_REGULATION_OF_LEUKOCYTE_MEDIATED_CYTOTOXICITY 0.0028986 0.0421001 -0.6273833 -2.735426 0 71 down
GO_REGULATION_OF_T_CELL_DIFFERENTIATION 0.0034965 0.0421001 -0.5641702 -2.731206 0 134 down
GO_POSITIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION 0.0034965 0.0421001 -0.5628371 -2.724752 0 134 down
GO_NEUTROPHIL_MIGRATION 0.0032051 0.0421001 -0.5907828 -2.718757 0 103 down
GO_POSITIVE_REGULATION_OF_T_CELL_PROLIFERATION 0.0030211 0.0421001 -0.5948595 -2.715885 0 91 down
GO_CD4_POSITIVE_ALPHA_BETA_T_CELL_DIFFERENTIATION 0.0028986 0.0421001 -0.6191160 -2.713679 0 72 down
GO_ANTIGEN_BINDING 0.0034965 0.0421001 -0.5581469 -2.702046 0 134 down
GO_CHEMOKINE_ACTIVITY 0.0025840 0.0421001 -0.7025948 -2.700800 0 41 down
GO_B_CELL_PROLIFERATION 0.0030030 0.0421001 -0.6078844 -2.694310 0 80 down
GO_REGULATION_OF_LEUKOCYTE_PROLIFERATION 0.0038168 0.0421001 -0.5212359 -2.688158 0 213 down
GO_REGULATION_OF_CELL_KILLING 0.0030488 0.0421001 -0.5873184 -2.673477 0 92 down
GO_POSITIVE_REGULATION_OF_CYTOKINE_BIOSYNTHETIC_PROCESS 0.0028011 0.0421001 -0.6231760 -2.670943 0 64 down
GO_POSITIVE_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY 0.0023364 0.0421001 -0.8299386 -2.669134 0 20 down
GO_POSITIVE_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION 0.0028653 0.0421001 -0.6344791 -2.660651 0 59 down
GO_T_CELL_MIGRATION 0.0029240 0.0421001 -0.6442188 -2.658192 0 57 down 
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
RPS14_DN.V1_UP 0.0040816 0.0192778 -0.5254744 -2.656141 0 182 down
NFE2L2.V2 0.0012516 0.0192778 0.5180769 2.548334 0 395 up
LEF1_UP.V1_UP 0.0040816 0.0192778 -0.4209208 -2.111485 0 179 down
P53_DN.V2_UP 0.0035714 0.0192778 -0.4315714 -2.102512 0 131 down
KRAS.LUNG_UP.V1_UP 0.0033333 0.0192778 -0.4370391 -2.089853 0 119 down
HOXA9_DN.V1_UP 0.0038023 0.0192778 -0.4154275 -2.073648 0 170 down
CYCLIN_D1_KE_.V1_DN 0.0038610 0.0192778 -0.4037184 -2.013409 0 173 down
SNF5_DN.V1_UP 0.0035971 0.0192778 -0.3899399 -1.939238 0 152 down
HINATA_NFKB_IMMU_INF 0.0025253 0.0192778 -0.6698299 -1.918285 0 14 down
RPS14_DN.V1_DN 0.0013495 0.0192778 0.4278120 1.913561 0 172 up
MYC_UP.V1_UP 0.0013569 0.0192778 0.4187909 1.850271 0 157 up
KRAS.PROSTATE_UP.V1_UP 0.0033445 0.0192778 -0.3847447 -1.843908 0 121 down
BRCA1_DN.V1_UP 0.0033784 0.0192778 -0.3818200 -1.804937 0 111 down
RAF_UP.V1_DN 0.0013175 0.0192778 0.3977018 1.797813 0 181 up
KRAS.KIDNEY_UP.V1_UP 0.0035336 0.0192778 -0.3672899 -1.784366 0 130 down
KRAS.300_UP.V1_UP 0.0035336 0.0192778 -0.3660896 -1.778534 0 130 down
ATM_DN.V1_DN 0.0035842 0.0192778 -0.3635004 -1.766754 0 132 down
KRAS.600.LUNG.BREAST_UP.V1_UP 0.0041841 0.0192778 -0.3335123 -1.746741 0 239 down
CAHOY_ASTROCYTIC 0.0028409 0.0192778 0.4189906 1.740658 1 98 up
WNT_UP.V1_DN 0.0036630 0.0192778 -0.3493423 -1.736856 0 155 down
KRAS.600_UP.V1_UP 0.0042553 0.0192778 -0.3313137 -1.734246 0 244 down
ALK_DN.V1_DN 0.0034130 0.0192778 -0.3587947 -1.731987 0 124 down
JNK_DN.V1_UP 0.0038168 0.0192778 -0.3486267 -1.727245 0 161 down
STK33_SKM_UP 0.0042017 0.0192778 -0.3285018 -1.724816 0 246 down
MEK_UP.V1_UP 0.0013298 0.0192778 0.3813490 1.717274 0 175 up
PRC2_SUZ12_UP.V1_UP 0.0039062 0.0192778 -0.3405697 -1.688198 0 166 down
KRAS.PROSTATE_UP.V1_DN 0.0034247 0.0192778 -0.3411692 -1.663528 0 129 down
PTEN_DN.V1_DN 0.0038610 0.0192778 -0.3341033 -1.652356 0 158 down
KRAS.300_UP.V1_DN 0.0034014 0.0192778 -0.3350458 -1.628433 0 128 down
CSR_LATE_UP.V1_UP 0.0013514 0.0192778 0.3657984 1.615817 0 156 up 
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN 0.0035336 0.0114714 -0.7135214 -3.491817 0 159 down
GSE19888_ADENOSINE_A3R_INH_PRETREAT_AND_ACT_BY_A3R_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP 0.0035587 0.0114714 -0.6463144 -3.248425 0 188 down
GSE10325_CD4_TCELL_VS_BCELL_UP 0.0035842 0.0114714 -0.6197352 -3.132816 0 190 down
GSE7509_UNSTIM_VS_IFNA_STIM_IMMATURE_DC_DN 0.0036232 0.0114714 -0.6293222 -3.111398 0 172 down
GSE7218_IGM_VS_IGG_SIGNAL_THGOUGH_ANTIGEN_BCELL_DN 0.0036101 0.0114714 -0.6240050 -3.059563 0 163 down
GSE7509_UNSTIM_VS_FCGRIIB_STIM_DC_DN 0.0036232 0.0114714 -0.6191177 -3.047398 0 168 down
GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_BCELL_UP 0.0035587 0.0114714 -0.6054333 -3.042953 0 188 down
GSE24634_IL4_VS_CTRL_TREATED_NAIVE_CD4_TCELL_DAY3_DN 0.0035842 0.0114714 -0.5908151 -2.963239 0 185 down
GSE43863_DAY6_EFF_VS_DAY150_MEM_LY6C_INT_CXCR5POS_CD4_TCELL_DN 0.0035714 0.0114714 -0.5868038 -2.938842 0 182 down
GSE37533_PPARG1_FOXP3_VS_FOXP3_TRANSDUCED_CD4_TCELL_DN 0.0035211 0.0114714 -0.5806766 -2.930705 0 189 down
GSE40685_TREG_VS_FOXP3_KO_TREG_PRECURSOR_DN 0.0035842 0.0114714 -0.5744553 -2.903922 0 190 down
GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_6H_DN 0.0036630 0.0114714 -0.5829122 -2.887333 0 176 down
GSE8835_CD4_VS_CD8_TCELL_CLL_PATIENT_UP 0.0035842 0.0114714 -0.5743073 -2.882743 0 187 down
GSE1460_INTRATHYMIC_T_PROGENITOR_VS_CD4_THYMOCYTE_DN 0.0035587 0.0114714 -0.5610281 -2.848183 0 194 down
GSE22886_NAIVE_CD8_TCELL_VS_MONOCYTE_UP 0.0035842 0.0114714 -0.5619664 -2.840789 0 190 down
GSE29618_BCELL_VS_PDC_UP 0.0035714 0.0114714 -0.5667642 -2.838479 0 182 down
GSE3039_NKT_CELL_VS_ALPHAALPHA_CD8_TCELL_DN 0.0035842 0.0114714 -0.5599443 -2.830568 0 190 down
GSE25677_MPL_VS_R848_STIM_BCELL_DN 0.0035971 0.0114714 -0.5699341 -2.822964 0 171 down
GSE19888_CTRL_VS_TCELL_MEMBRANES_ACT_MAST_CELL_PRETREAT_A3R_INH_DN 0.0035971 0.0114714 -0.5552837 -2.809553 0 191 down
GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_10H_DN 0.0036364 0.0114714 -0.5657334 -2.804538 0 175 down
GSE19888_ADENOSINE_A3R_INH_VS_ACT_WITH_INHIBITOR_PRETREATMENT_IN_MAST_CELL_UP 0.0035971 0.0114714 -0.5618989 -2.793575 0 178 down
GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_10H_DN 0.0036232 0.0114714 -0.5654195 -2.783087 0 168 down
GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_MYELOID_UP 0.0036364 0.0114714 -0.5555162 -2.777806 0 183 down
GSE16450_CTRL_VS_IFNA_6H_STIM_IMMATURE_NEURON_CELL_LINE_DN 0.0036364 0.0114714 -0.5598663 -2.775453 0 175 down
GSE26495_NAIVE_VS_PD1HIGH_CD8_TCELL_DN 0.0035714 0.0114714 -0.5537996 -2.773550 0 182 down
GSE22886_NAIVE_CD8_TCELL_VS_DC_UP 0.0035842 0.0114714 -0.5525306 -2.771223 0 185 down
GSE29618_BCELL_VS_PDC_DAY7_FLU_VACCINE_UP 0.0036630 0.0114714 -0.5581082 -2.770479 0 180 down
GSE5589_LPS_AND_IL10_VS_LPS_AND_IL6_STIM_IL6_KO_MACROPHAGE_45MIN_UP 0.0036364 0.0114714 -0.5530123 -2.765285 0 183 down
GSE7219_UNSTIM_VS_LPS_AND_ANTI_CD40_STIM_NIK_NFKB2_KO_DC_UP 0.0036765 0.0114714 -0.5606645 -2.764469 0 173 down
GSE2706_UNSTIM_VS_2H_LPS_AND_R848_DC_DN 0.0036630 0.0114714 -0.5553714 -2.756893 0 180 down 
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='SLC7A11 low vs high')

kable(fgp)
pathway pval padj ES NES nMoreExtreme size state
GO_T_CELL_RECEPTOR_COMPLEX 0.0030581 0.023721 -0.7926478 -3.567110 0 90 down
GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN 0.0035211 0.023721 -0.7135214 -3.540442 0 159 down
LEE_DIFFERENTIATING_T_LYMPHOCYTE 0.0035842 0.023721 -0.6954633 -3.490793 0 182 down
GNF2_ITGAL 0.0027248 0.023721 -0.8209758 -3.338700 0 52 down
FARMER_BREAST_CANCER_CLUSTER_1 0.0025840 0.023721 -0.8260042 -3.291005 0 47 down
MODULE_292 0.0032468 0.023721 -0.6854026 -3.268075 0 124 down
GSE19888_ADENOSINE_A3R_INH_PRETREAT_AND_ACT_BY_A3R_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP 0.0036232 0.023721 -0.6463144 -3.266836 0 188 down
REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 0.0034483 0.023721 -0.6435974 -3.240015 0 175 down
HALLMARK_ALLOGRAFT_REJECTION 0.0036232 0.023721 -0.6380091 -3.220860 0 187 down
GNF2_PTPN4 0.0025381 0.023721 -0.8135020 -3.187351 0 44 down
MODULE_171 0.0032573 0.023721 -0.6540173 -3.170551 0 131 down
GSE7509_UNSTIM_VS_IFNA_STIM_IMMATURE_DC_DN 0.0033784 0.023721 -0.6293222 -3.164707 0 172 down
GNF2_PTPRC 0.0028571 0.023721 -0.7557365 -3.144730 0 59 down
GNF2_CD7 0.0024752 0.023721 -0.8385679 -3.125328 0 36 down
GSE10325_CD4_TCELL_VS_BCELL_UP 0.0037313 0.023721 -0.6197352 -3.122983 0 190 down
GNF2_CASP1 0.0029412 0.023721 -0.6762542 -3.119118 0 103 down
MODULE_119 0.0033784 0.023721 -0.6374952 -3.117068 0 136 down
WINTER_HYPOXIA_DN 0.0026247 0.023721 -0.7893779 -3.105401 0 46 down
GSE7509_UNSTIM_VS_FCGRIIB_STIM_DC_DN 0.0034014 0.023721 -0.6191177 -3.097157 0 168 down
GSE7218_IGM_VS_IGG_SIGNAL_THGOUGH_ANTIGEN_BCELL_DN 0.0035211 0.023721 -0.6240050 -3.095438 0 163 down
MODULE_436 0.0032258 0.023721 -0.6480472 -3.082104 0 123 down
GNF2_HCK 0.0030303 0.023721 -0.6824185 -3.071791 0 89 down
GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_BCELL_UP 0.0036232 0.023721 -0.6054333 -3.060200 0 188 down
GNF2_ITGB2 0.0027248 0.023721 -0.7508068 -3.048282 0 51 down
MODULE_345 0.0030864 0.023721 -0.6454051 -3.047984 0 114 down
MODULE_208 0.0031546 0.023721 -0.6466721 -3.047519 0 117 down
LEE_EARLY_T_LYMPHOCYTE_DN 0.0028571 0.023721 -0.7390486 -3.042654 0 57 down
REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES 0.0028090 0.023721 -0.7393387 -3.035408 0 55 down
MODULE_361 0.0032258 0.023721 -0.6271367 -3.034143 0 130 down
HALLMARK_INTERFERON_ALPHA_RESPONSE 0.0029762 0.023721 -0.6655971 -3.024076 0 93 down